Aligning and housing miniature optic components is extremely difficult due to the high tolerances required for precision alignment.
One method is described in Day, J. C. C., Bennett, R., Smith, B, Kendall, C., Hutchings, J., Meaden, G. M., et al. (2009), A miniature confocal Raman probe for endoscopic use, Physics in medicine and biology, 54(23), 7077-87. doi: 10.1088/0031-9155/54/23/003.
In Day et al. the optical components are assembled on V-groove mounts on silicon motherboards before insertion into a protective sleeve. A problem with this arrangement is that the silicon motherboards are fragile and easy to break during assembly. Also, the optical components are unprotected during assembly until they are inserted into the protective sleeve.
Another method is described in Robert T. Kester, Todd Christenson, Rebecca Richards Kortum, and Tomasz S. Tkaczyk, “Low cost, high performance, self-aligning miniature optical systems,” Appl. Opt. 48, 3375-3384 (2009). Optical components are assembled inside a hypodermic tube and aligned with respect to the tube by self-aligning components. A problem with this arrangement is that it relies on the hypodermic tube providing a straight mechanical axis for aligning the optical components. In reality this tube may have some “waviness” to it so the optical components may not be precisely aligned with each other.